Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 4:8e3d95d7f342 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 07 Jul 2014 05:49:20 -0400 |
| parents | 79be0752711d |
| children | 35b55f1c0c59 |
| files | demultiplex.xml r_wrapper.sh tool_dependencies.xml trim.py |
| diffstat | 4 files changed, 330 insertions(+), 166 deletions(-) [+] |
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--- a/demultiplex.xml Tue Jul 01 08:27:57 2014 -0400 +++ b/demultiplex.xml Mon Jul 07 05:49:20 2014 -0400 @@ -16,156 +16,307 @@ <param name="id" type="text" label="ID" /> <param name="mid" type="select" label="Mid"> <option value="ACGAGTGCGT">MID-1</option> + <option value="ACGCACTCGT">MID-1 reverse complement</option> <option value="ACGCTCGACA">MID-2</option> + <option value="TGTCGAGCGT">MID-2 reverse complement</option> <option value="AGACGCACTC">MID-3</option> + <option value="GAGTGCGTCT">MID-3 reverse complement</option> <option value="AGCACTGTAG">MID-4</option> + <option value="CTACAGTGCT">MID-4 reverse complement</option> <option value="ATCAGACACG">MID-5</option> + <option value="CGTGTCTGAT">MID-5 reverse complement</option> <option value="ATATCGCGAG">MID-6</option> + <option value="CTCGCGATAT">MID-6 reverse complement</option> <option value="CGTGTCTCTA">MID-7</option> + <option value="TAGAGACACG">MID-7 reverse complement</option> <option value="CTCGCGTGTC">MID-8</option> - <option value="TCTCTATGCG">MID-10</option> - <option value="TGATACGTCT">MID-11</option> - <option value="CATAGTAGTG">MID-13</option> - <option value="CGAGAGATAC">MID-14</option> - <option value="ATACGACGTA">MID-15</option> - <option value="TCACGTACTA">MID-16</option> - <option value="CGTCTAGTAC">MID-17</option> - <option value="TCTACGTAGC">MID-18</option> - <option value="TGTACTACTC">MID-19</option> - <option value="ACGACTACAG">MID-20</option> - <option value="CGTAGACTAG">MID-21</option> - <option value="TACGAGTATG">MID-22</option> - <option value="TACTCTCGTG">MID-23</option> - <option value="TAGAGACGAG">MID-24</option> - <option value="TCGTCGCTCG">MID-25</option> - <option value="ACATACGCGT">MID-26</option> - <option value="ACGCGAGTAT">MID-27</option> - <option value="ACTACTATGT">MID-28</option> - <option value="ACTGTACAGT">MID-29</option> - <option value="AGACTATACT">MID-30</option> - <option value="AGCGTCGTCT">MID-31</option> - <option value="AGTACGCTAT">MID-32</option> - <option value="ATAGAGTACT">MID-33</option> - <option value="CACGCTACGT">MID-34</option> - <option value="CAGTAGACGT">MID-35</option> - <option value="CGACGTGACT">MID-36</option> - <option value="TACACACACT">MID-37</option> - <option value="TACACGTGAT">MID-38</option> - <option value="TACAGATCGT">MID-39</option> - <option value="TACGCTGTCT">MID-40</option> - <option value="TAGTGTAGAT">MID-41</option> - <option value="TCGATCACGT">MID-42</option> - <option value="TCGCACTAGT">MID-43</option> - <option value="TCTAGCGACT">MID-44</option> - <option value="TCTATACTAT">MID-45</option> - <option value="TGACGTATGT">MID-46</option> - <option value="TGTGAGTAGT">MID-47</option> - <option value="ACAGTATATA">MID-48</option> - <option value="ACGCGATCGA">MID-49</option> - <option value="ACTAGCAGTA">MID-50</option> - <option value="AGCTCACGTA">MID-51</option> - <option value="AGTATACATA">MID-52</option> - <option value="AGTCGAGAGA">MID-53</option> - <option value="AGTGCTACGA">MID-54</option> - <option value="CGATCGTATA">MID-55</option> - <option value="CGCAGTACGA">MID-56</option> - <option value="CGCGTATACA">MID-57</option> - <option value="CGTACAGTCA">MID-58</option> - <option value="CGTACTCAGA">MID-59</option> - <option value="CTACGCTCTA">MID-60</option> - <option value="CTATAGCGTA">MID-61</option> - <option value="TACGTCATCA">MID-62</option> - <option value="TAGTCGCATA">MID-63</option> - <option value="TATATATACA">MID-64</option> - <option value="TATGCTAGTA">MID-65</option> - <option value="TCACGCGAGA">MID-66</option> - <option value="TCGATAGTGA">MID-67</option> - <option value="TCGCTGCGTA">MID-68</option> - <option value="TCTGACGTCA">MID-69</option> - <option value="TGAGTCAGTA">MID-70</option> - <option value="TGTAGTGTGA">MID-71</option> - <option value="TGTCACACGA">MID-72</option> - <option value="TGTCGTCGCA">MID-73</option> - <option value="ACACATACGC">MID-74</option> - <option value="ACAGTCGTGC">MID-75</option> - <option value="ACATGACGAC">MID-76</option> - <option value="ACGACAGCTC">MID-77</option> - <option value="ACGTCTCATC">MID-78</option> - <option value="ACTCATCTAC">MID-79</option> - <option value="ACTCGCGCAC">MID-80</option> - <option value="AGAGCGTCAC">MID-81</option> - <option value="AGCGACTAGC">MID-82</option> - <option value="AGTAGTGATC">MID-83</option> - <option value="AGTGACACAC">MID-84</option> - <option value="AGTGTATGTC">MID-85</option> - <option value="ATAGATAGAC">MID-86</option> - <option value="ATATAGTCGC">MID-87</option> - <option value="ATCTACTGAC">MID-88</option> - <option value="CACGTAGATC">MID-89</option> - <option value="CACGTGTCGC">MID-90</option> - <option value="CATACTCTAC">MID-91</option> - <option value="CGACACTATC">MID-92</option> - <option value="CGAGACGCGC">MID-93</option> - <option value="CGTATGCGAC">MID-94</option> - <option value="CGTCGATCTC">MID-95</option> - <option value="CTACGACTGC">MID-96</option> - <option value="CTAGTCACTC">MID-97</option> - <option value="CTCTACGCTC">MID-98</option> - <option value="CTGTACATAC">MID-99</option> - <option value="TAGACTGCAC">MID-100</option> - <option value="TAGCGCGCGC">MID-101</option> - <option value="TAGCTCTATC">MID-102</option> - <option value="TATAGACATC">MID-103</option> - <option value="TATGATACGC">MID-104</option> - <option value="TCACTCATAC">MID-105</option> - <option value="TCATCGAGTC">MID-106</option> - <option value="TCGAGCTCTC">MID-107</option> - <option value="TCGCAGACAC">MID-108</option> - <option value="TCTGTCTCGC">MID-109</option> - <option value="TGAGTGACGC">MID-110</option> - <option value="TGATGTGTAC">MID-111</option> - <option value="TGCTATAGAC">MID-112</option> - <option value="TGCTCGCTAC">MID-113</option> - <option value="ACGTGCAGCG">MID-114</option> - <option value="ACTCACAGAG">MID-115</option> - <option value="AGACTCAGCG">MID-116</option> - <option value="AGAGAGTGTG">MID-117</option> - <option value="AGCTATCGCG">MID-118</option> - <option value="AGTCTGACTG">MID-119</option> - <option value="AGTGAGCTCG">MID-120</option> - <option value="ATAGCTCTCG">MID-121</option> - <option value="ATCACGTGCG">MID-122</option> - <option value="ATCGTAGCAG">MID-123</option> - <option value="ATCGTCTGTG">MID-124</option> - <option value="ATGTACGATG">MID-125</option> - <option value="ATGTGTCTAG">MID-126</option> - <option value="CACACGATAG">MID-127</option> - <option value="CACTCGCACG">MID-128</option> - <option value="CAGACGTCTG">MID-129</option> - <option value="CAGTACTGCG">MID-130</option> - <option value="CGACAGCGAG">MID-131</option> - <option value="CGATCTGTCG">MID-132</option> - <option value="CGCGTGCTAG">MID-133</option> - <option value="CGCTCGAGTG">MID-134</option> - <option value="CGTGATGACG">MID-135</option> - <option value="CTATGTACAG">MID-136</option> - <option value="CTCGATATAG">MID-137</option> - <option value="CTCGCACGCG">MID-138</option> - <option value="CTGCGTCACG">MID-139</option> - <option value="CTGTGCGTCG">MID-140</option> - <option value="TAGCATACTG">MID-141</option> - <option value="TATACATGTG">MID-142</option> - <option value="TATCACTCAG">MID-143</option> - <option value="TATCTGATAG">MID-144</option> - <option value="TCGTGACATG">MID-145</option> - <option value="TCTGATCGAG">MID-146</option> - <option value="TGACATCTCG">MID-147</option> - <option value="TGAGCTAGAG">MID-148</option> - <option value="TGATAGAGCG">MID-149</option> - <option value="TGCGTGTGCG">MID-150</option> - <option value="TGCTAGTCAG">MID-151</option> - <option value="TGTATCACAG">MID-152</option> - <option value="TGTGCGCGTG">MID-153</option> + <option value="GACACGCGAG">MID-8 reverse complement</option> + <option value="TCTCTATGCG">MID-9</option> + <option value="CGCATAGAGA">MID-9 reverse complement</option> + <option value="TGATACGTCT">MID-10</option> + <option value="AGACGTATCA">MID-10 reverse complement</option> + <option value="CATAGTAGTG">MID-11</option> + <option value="CACTACTATG">MID-11 reverse complement</option> + <option value="CGAGAGATAC">MID-12</option> + <option value="GTATCTCTCG">MID-12 reverse complement</option> + <option value="ATACGACGTA">MID-13</option> + <option value="TACGTCGTAT">MID-13 reverse complement</option> + <option value="TCACGTACTA">MID-14</option> + <option value="TAGTACGTGA">MID-14 reverse complement</option> + <option value="CGTCTAGTAC">MID-15</option> + <option value="GTACTAGACG">MID-15 reverse complement</option> + <option value="TCTACGTAGC">MID-16</option> + <option value="GCTACGTAGA">MID-16 reverse complement</option> + <option value="TGTACTACTC">MID-17</option> + <option value="GAGTAGTACA">MID-17 reverse complement</option> + <option value="ACGACTACAG">MID-18</option> + <option value="CTGTAGTCGT">MID-18 reverse complement</option> + <option value="CGTAGACTAG">MID-19</option> + <option value="CTAGTCTACG">MID-19 reverse complement</option> + <option value="TACGAGTATG">MID-20</option> + <option value="CATACTCGTA">MID-20 reverse complement</option> + <option value="TACTCTCGTG">MID-21</option> + <option value="CACGAGAGTA">MID-21 reverse complement</option> + <option value="TAGAGACGAG">MID-22</option> + <option value="CTCGTCTCTA">MID-22 reverse complement</option> + <option value="TCGTCGCTCG">MID-23</option> + <option value="CGAGCGACGA">MID-23 reverse complement</option> + <option value="ACATACGCGT">MID-24</option> + <option value="ACGCGTATGT">MID-24 reverse complement</option> + <option value="ACGCGAGTAT">MID-25</option> + <option value="ATACTCGCGT">MID-25 reverse complement</option> + <option value="ACTACTATGT">MID-26</option> + <option value="ACATAGTAGT">MID-26 reverse complement</option> + <option value="ACTGTACAGT">MID-27</option> + <option value="ACTGTACAGT">MID-27 reverse complement</option> + <option value="AGACTATACT">MID-28</option> + <option value="AGTATAGTCT">MID-28 reverse complement</option> + <option value="AGCGTCGTCT">MID-29</option> + <option value="AGACGACGCT">MID-29 reverse complement</option> + <option value="AGTACGCTAT">MID-30</option> + <option value="ATAGCGTACT">MID-30 reverse complement</option> + <option value="ATAGAGTACT">MID-31</option> + <option value="AGTACTCTAT">MID-31 reverse complement</option> + <option value="CACGCTACGT">MID-32</option> + <option value="ACGTAGCGTG">MID-32 reverse complement</option> + <option value="CAGTAGACGT">MID-33</option> + <option value="ACGTCTACTG">MID-33 reverse complement</option> + <option value="CGACGTGACT">MID-34</option> + <option value="AGTCACGTCG">MID-34 reverse complement</option> + <option value="TACACACACT">MID-35</option> + <option value="AGTGTGTGTA">MID-35 reverse complement</option> + <option value="TACACGTGAT">MID-36</option> + <option value="ATCACGTGTA">MID-36 reverse complement</option> + <option value="TACAGATCGT">MID-37</option> + <option value="ACGATCTGTA">MID-37 reverse complement</option> + <option value="TACGCTGTCT">MID-38</option> + <option value="AGACAGCGTA">MID-38 reverse complement</option> + <option value="TAGTGTAGAT">MID-39</option> + <option value="ATCTACACTA">MID-39 reverse complement</option> + <option value="TCGATCACGT">MID-40</option> + <option value="ACGTGATCGA">MID-40 reverse complement</option> + <option value="TCGCACTAGT">MID-41</option> + <option value="ACTAGTGCGA">MID-41 reverse complement</option> + <option value="TCTAGCGACT">MID-42</option> + <option value="AGTCGCTAGA">MID-42 reverse complement</option> + <option value="TCTATACTAT">MID-43</option> + <option value="ATAGTATAGA">MID-43 reverse complement</option> + <option value="TGACGTATGT">MID-44</option> + <option value="ACATACGTCA">MID-44 reverse complement</option> + <option value="TGTGAGTAGT">MID-45</option> + <option value="ACTACTCACA">MID-45 reverse complement</option> + <option value="ACAGTATATA">MID-46</option> + <option value="TATATACTGT">MID-46 reverse complement</option> + <option value="ACGCGATCGA">MID-47</option> + <option value="TCGATCGCGT">MID-47 reverse complement</option> + <option value="ACTAGCAGTA">MID-48</option> + <option value="TACTGCTAGT">MID-48 reverse complement</option> + <option value="AGCTCACGTA">MID-49</option> + <option value="TACGTGAGCT">MID-49 reverse complement</option> + <option value="AGTATACATA">MID-50</option> + <option value="TATGTATACT">MID-50 reverse complement</option> + <option value="AGTCGAGAGA">MID-51</option> + <option value="TCTCTCGACT">MID-51 reverse complement</option> + <option value="AGTGCTACGA">MID-52</option> + <option value="TCGTAGCACT">MID-52 reverse complement</option> + <option value="CGATCGTATA">MID-53</option> + <option value="TATACGATCG">MID-53 reverse complement</option> + <option value="CGCAGTACGA">MID-54</option> + <option value="TCGTACTGCG">MID-54 reverse complement</option> + <option value="CGCGTATACA">MID-55</option> + <option value="TGTATACGCG">MID-55 reverse complement</option> + <option value="CGTACAGTCA">MID-56</option> + <option value="TGACTGTACG">MID-56 reverse complement</option> + <option value="CGTACTCAGA">MID-57</option> + <option value="TCTGAGTACG">MID-57 reverse complement</option> + <option value="CTACGCTCTA">MID-58</option> + <option value="TAGAGCGTAG">MID-58 reverse complement</option> + <option value="CTATAGCGTA">MID-59</option> + <option value="TACGCTATAG">MID-59 reverse complement</option> + <option value="TACGTCATCA">MID-60</option> + <option value="TGATGACGTA">MID-60 reverse complement</option> + <option value="TAGTCGCATA">MID-61</option> + <option value="TATGCGACTA">MID-61 reverse complement</option> + <option value="TATATATACA">MID-62</option> + <option value="TGTATATATA">MID-62 reverse complement</option> + <option value="TATGCTAGTA">MID-63</option> + <option value="TACTAGCATA">MID-63 reverse complement</option> + <option value="TCACGCGAGA">MID-64</option> + <option value="TCTCGCGTGA">MID-64 reverse complement</option> + <option value="TCGATAGTGA">MID-65</option> + <option value="TCACTATCGA">MID-65 reverse complement</option> + <option value="TCGCTGCGTA">MID-66</option> + <option value="TACGCAGCGA">MID-66 reverse complement</option> + <option value="TCTGACGTCA">MID-67</option> + <option value="TGACGTCAGA">MID-67 reverse complement</option> + <option value="TGAGTCAGTA">MID-68</option> + <option value="TACTGACTCA">MID-68 reverse complement</option> + <option value="TGTAGTGTGA">MID-69</option> + <option value="TCACACTACA">MID-69 reverse complement</option> + <option value="TGTCACACGA">MID-70</option> + <option value="TCGTGTGACA">MID-70 reverse complement</option> + <option value="TGTCGTCGCA">MID-71</option> + <option value="TGCGACGACA">MID-71 reverse complement</option> + <option value="ACACATACGC">MID-72</option> + <option value="GCGTATGTGT">MID-72 reverse complement</option> + <option value="ACAGTCGTGC">MID-73</option> + <option value="GCACGACTGT">MID-73 reverse complement</option> + <option value="ACATGACGAC">MID-74</option> + <option value="GTCGTCATGT">MID-74 reverse complement</option> + <option value="ACGACAGCTC">MID-75</option> + <option value="GAGCTGTCGT">MID-75 reverse complement</option> + <option value="ACGTCTCATC">MID-76</option> + <option value="GATGAGACGT">MID-76 reverse complement</option> + <option value="ACTCATCTAC">MID-77</option> + <option value="GTAGATGAGT">MID-77 reverse complement</option> + <option value="ACTCGCGCAC">MID-78</option> + <option value="GTGCGCGAGT">MID-78 reverse complement</option> + <option value="AGAGCGTCAC">MID-79</option> + <option value="GTGACGCTCT">MID-79 reverse complement</option> + <option value="AGCGACTAGC">MID-80</option> + <option value="GCTAGTCGCT">MID-80 reverse complement</option> + <option value="AGTAGTGATC">MID-81</option> + <option value="GATCACTACT">MID-81 reverse complement</option> + <option value="AGTGACACAC">MID-82</option> + <option value="GTGTGTCACT">MID-82 reverse complement</option> + <option value="AGTGTATGTC">MID-83</option> + <option value="GACATACACT">MID-83 reverse complement</option> + <option value="ATAGATAGAC">MID-84</option> + <option value="GTCTATCTAT">MID-84 reverse complement</option> + <option value="ATATAGTCGC">MID-85</option> + <option value="GCGACTATAT">MID-85 reverse complement</option> + <option value="ATCTACTGAC">MID-86</option> + <option value="GTCAGTAGAT">MID-86 reverse complement</option> + <option value="CACGTAGATC">MID-87</option> + <option value="GATCTACGTG">MID-87 reverse complement</option> + <option value="CACGTGTCGC">MID-88</option> + <option value="GCGACACGTG">MID-88 reverse complement</option> + <option value="CATACTCTAC">MID-89</option> + <option value="GTAGAGTATG">MID-89 reverse complement</option> + <option value="CGACACTATC">MID-90</option> + <option value="GATAGTGTCG">MID-90 reverse complement</option> + <option value="CGAGACGCGC">MID-91</option> + <option value="GCGCGTCTCG">MID-91 reverse complement</option> + <option value="CGTATGCGAC">MID-92</option> + <option value="GTCGCATACG">MID-92 reverse complement</option> + <option value="CGTCGATCTC">MID-93</option> + <option value="GAGATCGACG">MID-93 reverse complement</option> + <option value="CTACGACTGC">MID-94</option> + <option value="GCAGTCGTAG">MID-94 reverse complement</option> + <option value="CTAGTCACTC">MID-95</option> + <option value="GAGTGACTAG">MID-95 reverse complement</option> + <option value="CTCTACGCTC">MID-96</option> + <option value="GAGCGTAGAG">MID-96 reverse complement</option> + <option value="CTGTACATAC">MID-97</option> + <option value="GTATGTACAG">MID-97 reverse complement</option> + <option value="TAGACTGCAC">MID-98</option> + <option value="GTGCAGTCTA">MID-98 reverse complement</option> + <option value="TAGCGCGCGC">MID-99</option> + <option value="GCGCGCGCTA">MID-99 reverse complement</option> + <option value="TAGCTCTATC">MID-100</option> + <option value="GATAGAGCTA">MID-100 reverse complement</option> + <option value="TATAGACATC">MID-101</option> + <option value="GATGTCTATA">MID-101 reverse complement</option> + <option value="TATGATACGC">MID-102</option> + <option value="GCGTATCATA">MID-102 reverse complement</option> + <option value="TCACTCATAC">MID-103</option> + <option value="GTATGAGTGA">MID-103 reverse complement</option> + <option value="TCATCGAGTC">MID-104</option> + <option value="GACTCGATGA">MID-104 reverse complement</option> + <option value="TCGAGCTCTC">MID-105</option> + <option value="GAGAGCTCGA">MID-105 reverse complement</option> + <option value="TCGCAGACAC">MID-106</option> + <option value="GTGTCTGCGA">MID-106 reverse complement</option> + <option value="TCTGTCTCGC">MID-107</option> + <option value="GCGAGACAGA">MID-107 reverse complement</option> + <option value="TGAGTGACGC">MID-108</option> + <option value="GCGTCACTCA">MID-108 reverse complement</option> + <option value="TGATGTGTAC">MID-109</option> + <option value="GTACACATCA">MID-109 reverse complement</option> + <option value="TGCTATAGAC">MID-110</option> + <option value="GTCTATAGCA">MID-110 reverse complement</option> + <option value="TGCTCGCTAC">MID-111</option> + <option value="GTAGCGAGCA">MID-111 reverse complement</option> + <option value="ACGTGCAGCG">MID-112</option> + <option value="CGCTGCACGT">MID-112 reverse complement</option> + <option value="ACTCACAGAG">MID-113</option> + <option value="CTCTGTGAGT">MID-113 reverse complement</option> + <option value="AGACTCAGCG">MID-114</option> + <option value="CGCTGAGTCT">MID-114 reverse complement</option> + <option value="AGAGAGTGTG">MID-115</option> + <option value="CACACTCTCT">MID-115 reverse complement</option> + <option value="AGCTATCGCG">MID-116</option> + <option value="CGCGATAGCT">MID-116 reverse complement</option> + <option value="AGTCTGACTG">MID-117</option> + <option value="CAGTCAGACT">MID-117 reverse complement</option> + <option value="AGTGAGCTCG">MID-118</option> + <option value="CGAGCTCACT">MID-118 reverse complement</option> + <option value="ATAGCTCTCG">MID-119</option> + <option value="CGAGAGCTAT">MID-119 reverse complement</option> + <option value="ATCACGTGCG">MID-120</option> + <option value="CGCACGTGAT">MID-120 reverse complement</option> + <option value="ATCGTAGCAG">MID-121</option> + <option value="CTGCTACGAT">MID-121 reverse complement</option> + <option value="ATCGTCTGTG">MID-122</option> + <option value="CACAGACGAT">MID-122 reverse complement</option> + <option value="ATGTACGATG">MID-123</option> + <option value="CATCGTACAT">MID-123 reverse complement</option> + <option value="ATGTGTCTAG">MID-124</option> + <option value="CTAGACACAT">MID-124 reverse complement</option> + <option value="CACACGATAG">MID-125</option> + <option value="CTATCGTGTG">MID-125 reverse complement</option> + <option value="CACTCGCACG">MID-126</option> + <option value="CGTGCGAGTG">MID-126 reverse complement</option> + <option value="CAGACGTCTG">MID-127</option> + <option value="CAGACGTCTG">MID-127 reverse complement</option> + <option value="CAGTACTGCG">MID-128</option> + <option value="CGCAGTACTG">MID-128 reverse complement</option> + <option value="CGACAGCGAG">MID-129</option> + <option value="CTCGCTGTCG">MID-129 reverse complement</option> + <option value="CGATCTGTCG">MID-130</option> + <option value="CGACAGATCG">MID-130 reverse complement</option> + <option value="CGCGTGCTAG">MID-131</option> + <option value="CTAGCACGCG">MID-131 reverse complement</option> + <option value="CGCTCGAGTG">MID-132</option> + <option value="CACTCGAGCG">MID-132 reverse complement</option> + <option value="CGTGATGACG">MID-133</option> + <option value="CGTCATCACG">MID-133 reverse complement</option> + <option value="CTATGTACAG">MID-134</option> + <option value="CTGTACATAG">MID-134 reverse complement</option> + <option value="CTCGATATAG">MID-135</option> + <option value="CTATATCGAG">MID-135 reverse complement</option> + <option value="CTCGCACGCG">MID-136</option> + <option value="CGCGTGCGAG">MID-136 reverse complement</option> + <option value="CTGCGTCACG">MID-137</option> + <option value="CGTGACGCAG">MID-137 reverse complement</option> + <option value="CTGTGCGTCG">MID-138</option> + <option value="CGACGCACAG">MID-138 reverse complement</option> + <option value="TAGCATACTG">MID-139</option> + <option value="CAGTATGCTA">MID-139 reverse complement</option> + <option value="TATACATGTG">MID-140</option> + <option value="CACATGTATA">MID-140 reverse complement</option> + <option value="TATCACTCAG">MID-141</option> + <option value="CTGAGTGATA">MID-141 reverse complement</option> + <option value="TATCTGATAG">MID-142</option> + <option value="CTATCAGATA">MID-142 reverse complement</option> + <option value="TCGTGACATG">MID-143</option> + <option value="CATGTCACGA">MID-143 reverse complement</option> + <option value="TCTGATCGAG">MID-144</option> + <option value="CTCGATCAGA">MID-144 reverse complement</option> + <option value="TGACATCTCG">MID-145</option> + <option value="CGAGATGTCA">MID-145 reverse complement</option> + <option value="TGAGCTAGAG">MID-146</option> + <option value="CTCTAGCTCA">MID-146 reverse complement</option> + <option value="TGATAGAGCG">MID-147</option> + <option value="CGCTCTATCA">MID-147 reverse complement</option> + <option value="TGCGTGTGCG">MID-148</option> + <option value="CGCACACGCA">MID-148 reverse complement</option> + <option value="TGCTAGTCAG">MID-149</option> + <option value="CTGACTAGCA">MID-149 reverse complement</option> + <option value="TGTATCACAG">MID-150</option> + <option value="CTGTGATACA">MID-150 reverse complement</option> + <option value="TGTGCGCGTG">MID-151</option> + <option value="CACGCGCACA">MID-151 reverse complement</option> </param> </repeat>
--- a/r_wrapper.sh Tue Jul 01 08:27:57 2014 -0400 +++ b/r_wrapper.sh Mon Jul 07 05:49:20 2014 -0400 @@ -38,4 +38,4 @@ python $dir/trim.py --input $file.fasta --output ${file}_trimmed.fasta --start $trim_start --end $trim_end echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td></tr>" >> $output done < output.txt -echo "</tbody></body><a href='trimmed.fasta'>Original fasta after trim</a></html>" >> $output +echo "</tbody></body></html>" >> $output
--- a/tool_dependencies.xml Tue Jul 01 08:27:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="fastx_toolkit" version="0.0.13"> - <repository changeset_revision="1cd326991d32" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/trim.py Tue Jul 01 08:27:57 2014 -0400 +++ b/trim.py Mon Jul 07 05:49:20 2014 -0400 @@ -2,8 +2,8 @@ #docs.python.org/dev/library/argparse.html parser = argparse.ArgumentParser() -parser.add_argument("--input", help="Input folder with files") -parser.add_argument("--output", help="Output file") +parser.add_argument("--input", help="Input fasta") +parser.add_argument("--output", help="Output fasta") parser.add_argument("--start", help="How many nucleotides to trim from the start", type=int) parser.add_argument("--end", help="How many nucleotides to trim from the end", type=int) @@ -11,25 +11,44 @@ start = int(args.start) end = int(args.end) -if end <= 0: +if end <= 0 and start <= 0: import shutil shutil.copy(args.input, args.output) import sys sys.exit() + + currentSeq = "" currentId = "" -with open(args.input, 'r') as i: - with open(args.output, 'w') as o: - for line in i.readlines(): - if line[0] is ">": - if currentSeq is not "" or currentId is not "": - o.write(currentId) - o.write(currentSeq[start:-end] + "\n") - currentId = line - currentSeq = "" - else: - currentSeq += line.rstrip() - o.write(currentId) - o.write(currentSeq.rstrip()[start:-end] + "\n") +if end is 0: + with open(args.input, 'r') as i: + with open(args.output, 'w') as o: + for line in i.readlines(): + if line[0] is ">": + currentSeq = currentSeq[start:] + if currentSeq is not "" and currentId is not "": + o.write(currentId) + o.write(currentSeq + "\n") + currentId = line + currentSeq = "" + else: + currentSeq += line.rstrip() + o.write(currentId) + o.write(currentSeq[start:] + "\n") +else: + with open(args.input, 'r') as i: + with open(args.output, 'w') as o: + for line in i.readlines(): + if line[0] is ">": + currentSeq = currentSeq[start:-end] + if currentSeq is not "" and currentId is not "": + o.write(currentId) + o.write(currentSeq + "\n") + currentId = line + currentSeq = "" + else: + currentSeq += line.rstrip() + o.write(currentId) + o.write(currentSeq[start:-end] + "\n")