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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 82ae2fa7e7a4a51f7583c6a95bdafc5f843c7c3b
author mbernt
date Mon, 07 Aug 2023 13:52:15 +0000
parents
children
files getLongestORF.py longORF.xml test-data/test_input.fasta test-data/test_output.fasta test-data/test_output.tab
diffstat 5 files changed, 295 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getLongestORF.py	Mon Aug 07 13:52:15 2023 +0000
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+
+#example:
+#>STRG.1.1(-)_1 [10 - 69]
+#GGNHHTLGGKKTFSYTHPPC
+#>STRG.1.1(-)_2 [3 - 80]
+#FLRGEPPHIGGKKDIFLHPPTLLKGR
+
+#output1: fasta file with all longest ORFs per transcript
+#output2: table with information about seqID, transcript, start, end, strand, length, sense, longest? for all ORFs
+
+import sys,re;
+
+def findlongestOrf(transcriptDict,old_seqID):
+	#write for previous seqID
+	prevTranscript = transcriptDict[old_seqID];
+	i_max = 0;
+	transcript = old_seqID.split("(")[0]
+
+	#find longest orf in transcript
+	for i in range(0,len(prevTranscript)):
+		if(prevTranscript[i][2] >= prevTranscript[i_max][2]):
+			i_max = i;
+
+	for i in range(0,len(prevTranscript)):
+		prevORFstart = prevTranscript[i][0];
+		prevORFend = prevTranscript[i][1];
+		prevORFlength = prevTranscript[i][2];
+		header = prevTranscript[i][3];
+		strand = re.search('\(([+-]+)\)',header).group(1);
+		
+		output = str(header) + "\t" + str(transcript) + "\t" + str(prevORFstart) + "\t" + str(prevORFend) + "\t" + str(prevORFlength) + "\t" + str(strand);
+		if (prevORFend - prevORFstart > 0):
+			output+="\tnormal";
+		else:
+			output+="\treverse_sense";
+		if(i == i_max):
+			output += "\ty\n";
+		else:
+			output += "\tn\n";
+
+		OUTPUT_ORF_SUMMARY.write(output);
+
+	transcriptDict.pop(old_seqID, None);
+	return None;
+
+#-----------------------------------------------------------------------------------------------------
+
+INPUT = open(sys.argv[1],"r");
+OUTPUT_FASTA = open(sys.argv[2],"w");
+OUTPUT_ORF_SUMMARY = open(sys.argv[3],"w");
+
+seqID = "";
+old_seqID = "";
+lengthDict = {};
+seqDict = {};
+headerDict = {};
+transcriptDict = {};
+
+skip = False;
+
+OUTPUT_ORF_SUMMARY.write("seqID\ttranscript\torf_start\torf_end\tlength\tstrand\tsense\tlongest\n");
+
+for line in INPUT:
+	line = line.strip();
+	if(re.match(">",line)): #header
+		header = line.split(">")[1].split(" ")[0]
+		seqID = "_".join(line.split(">")[1].split("_")[:-1])
+		ORFstart = int (re.search('\ \[(\d+)\ -', line).group(1));
+		ORFend = int (re.search('-\ (\d+)\]',line).group(1));
+		length = abs(ORFend - ORFstart);
+
+		if(seqID not in transcriptDict and old_seqID != ""): #new transcript
+			findlongestOrf(transcriptDict,old_seqID);
+			
+		if seqID not in transcriptDict:
+			transcriptDict[seqID] = [];
+
+		transcriptDict[seqID].append([ORFstart,ORFend,length,header]);
+
+		if(seqID not in lengthDict and old_seqID != ""): #new transcript
+			#write FASTA
+			OUTPUT_FASTA.write(headerDict[old_seqID]+"\n"+seqDict[old_seqID]+"\n");
+			#delete old dict entry
+			headerDict.pop(old_seqID, None);
+			seqDict.pop(old_seqID, None);
+			lengthDict.pop(old_seqID, None);
+		#if several longest sequences exist with the same length, the dictionary saves the last occuring.
+		if(seqID not in lengthDict or length >= lengthDict[seqID]):
+			headerDict[seqID] = line;
+			lengthDict[seqID] = length;
+			seqDict[seqID] = "";
+			skip = False;
+		else:
+			skip = True;
+			next;
+		old_seqID = seqID;
+	elif(skip):
+		next;
+	else:
+		seqDict[seqID] += line;
+
+OUTPUT_FASTA.write(headerDict[old_seqID]+"\n"+seqDict[old_seqID]);
+findlongestOrf(transcriptDict,old_seqID);
+
+INPUT.close();
+OUTPUT_FASTA.close();
+OUTPUT_ORF_SUMMARY.close();
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/longORF.xml	Mon Aug 07 13:52:15 2023 +0000
@@ -0,0 +1,35 @@
+<tool id="longORF" name="Obtain longest ORFs" version="0.3.0">
+    <description> in six-frame translations</description>
+    <command><![CDATA[
+        python $__tool_directory__/getLongestORF.py $input $output_longestORF $output_ORFs
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" format="fasta" type="data" label="sequences"/>
+    </inputs>
+    <outputs>
+        <data name="output_longestORF" format="fasta"/>
+        <data name="output_ORFs" format="tabular"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="test_input.fasta"/>
+            <output name="output_longestORF" file="test_output.fasta"/>
+            <output name="output_ORFs" file="test_output.tab"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool identifies the longest Open Reading Frames within the six-frame translations of a set of sequences. 
+
+**Input**
+
+It takes an amino acid fasta file with all open reading frames (+ and - strand) listed by the correspondng transcript. The tool is designed to process the output of the Galaxy tool "getorf" from the EMBOSS package.
+
+**Output**
+
+For each transcript, the respected longest ORF is identified and listed in fasta format. Furthermore, table with information about seqID, start, end, length, orientation, longest for all ORFs is given.]]>
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.fasta	Mon Aug 07 13:52:15 2023 +0000
@@ -0,0 +1,100 @@
+>STRG.4.1(-)_1 [3 - 77] 
+PNHCLRGHESPETRQSPLSGKRIPS
+>STRG.4.1(-)_2 [59 - 88] 
+WKEDPLIVCP
+>STRG.4.1(-)_3 [92 - 127] 
+WNRERYFQGFGL
+>STRG.4.1(-)_4 [131 - 268] 
+LPTQKQKDRWGTHTLERFGFTVPTMPAVISLFTETNPSSQITSTQD
+>STRG.4.1(-)_5 [81 - 332] 
+SAPDGIGKDTSRGSDYNCQPRNKRTAGGLTPWRDLGSQCPQCQRLFHYLRRRIPPVRSLQ
+LKTKFWRHPDHLGTHRLLGVPAEN
+>STRG.4.1(-)_6 [272 - 379] 
+VLETPRPSGHAQATWGSCGELSSQMQMESAMMPSTW
+>STRG.4.1(-)_7 [366 - 437] 
+CPLRGRGTGRSHGAAGHAVPPNRH
+>STRG.4.1(-)_8 [465 - 518] 
+KRYGMCCVYLDKFVGGCG
+>STRG.4.1(-)_9 [383 - 565] 
+GHWTKPWSCGACGTTQSTLRPRSSEPIKALRNVLCLPGQICWWLWLSWMGRNKKPWTWFP
+W
+>STRG.4.1(-)_10 [599 - 664] 
+SSEWWSWWTSASSPSTPVGRSS
+>STRG.4.1(-)_11 [522 - 665] 
+AGWVGTRSLGPGSLGDQRGPGGALPDRRSGGRGGHRRHPHQLPWGEAA
+>STRG.4.1(-)_12 [1 - 666] 
+DPTTVYVDMRALRHDRVRLVERGSPHSLPLMESGKILPGVRIIIANPETKGPLGDSHLGE
+IWVHSAHNASGYFTIYGDESLQSDHFNSRLSFGDTQTIWARTGYLGFLRRTELTDANGER
+HDALYVVGALDEAMELRGMRYHPIDIETSVIRAHKSVTECAVFTWTNLLVVVVELDGSEQ
+EALDLVPLVTNVVLEEHYLIVGVVVVVDIGVIPINSRGEKQR
+>STRG.4.1(-)_13 [665 - 594] (REVERSE SENSE) 
+RCFSPRELMGMTPMSTTTTTPTIR
+>STRG.4.1(-)_14 [631 - 491] (REVERSE SENSE) 
+RRCPPRPPLRRSGSAPPGPRWSPREPGPRLLVPTHPAQPQPPTNLSR
+>STRG.4.1(-)_15 [590 - 375] (REVERSE SENSE) 
+CSSRTTLVTKGTRSKASCSDPSSSTTTTNKFVQVNTAHSVTLLWALMTEVSMSIGWYRMP
+RSSMASSSAPTT
+>STRG.4.1(-)_16 [448 - 341] (REVERSE SENSE) 
+PRSQCRLGGTACPAAPWLRPVPLPRRGHHGALHLHL
+>STRG.4.1(-)_17 [371 - 312] (REVERSE SENSE) 
+RASWRSPFASVSSVLRRNPK
+>STRG.4.1(-)_18 [666 - 271] (REVERSE SENSE) 
+ALLLPTGVDGDDADVHHDHHSDDQVVLLQDHVGHQGNQVQGFLFRPIQLNHNHQQICPGK
+HSTFRNAFMGSDDRGLNVDWVVPHAPQLHGFVQCPYHVEGIMALSICICELSSPQEPQVA
+CACPDGLGVSKT
+>STRG.4.1(-)_19 [337 - 260] (REVERSE SENSE) 
+AQFSAGTPSSLCVPRWSGCLQNLVLS
+>STRG.4.1(-)_20 [308 - 255] (REVERSE SENSE) 
+PVRAQMVWVSPKLSLELK
+>STRG.4.1(-)_21 [256 - 224] (REVERSE SENSE) 
+SDLTGGIRLRK
+>STRG.4.1(-)_22 [246 - 169] (REVERSE SENSE) 
+LEGFVSVNSEITAGIVGTVNPNLSKV
+>STRG.4.1(-)_23 [217 - 128] (REVERSE SENSE) 
+NNRWHCGHCEPKSLQGVSPPAVLLFLGWQL
+>STRG.4.1(-)_24 [188 - 78] (REVERSE SENSE) 
+TQISPRCESPSGPFVSGLAIIIRTPGSIFPDSIRGRL
+>STRG.4.1(-)_25 [165 - 58] (REVERSE SENSE) 
+VPQRSFCFWVGNYNPNPWKYLSRFHQGQTMRGSSFH
+>STRG.4.1(-)_26 [74 - 18] (REVERSE SENSE) 
+GDPLSTKRTLSCLRALMST
+>STRG.4.1(-)_27 [124 - 2] (REVERSE SENSE) 
+SEPLEVSFPIPSGADYEGILFPLSGLCRVSGLSCPRRQWLG
+>STRG.4.1(-)_28 [54 - 1] (REVERSE SENSE) 
+ADSVVSQGSHVHVDSGWV
+>STRG.6.1(-)_1 [1 - 63] 
+NWDASWRKDVSRSHQCLLPFH
+>STRG.6.1(-)_2 [24 - 182] 
+RCLTQPPVPSAVPLSCSVNFTPLEKWPSAWTLTVDWDLSSGASAVCILGTSPS
+>STRG.6.1(-)_3 [94 - 195] 
+RSGHLPGPLLWTGICPLVPLQCVFWAPVHPDPAL
+>STRG.6.1(-)_4 [186 - 233] 
+SRPLSWKPTPPCGFLP
+>STRG.6.1(-)_5 [2 - 250] 
+TGMLAGVKMSHAATSAFCRSIKLQCELYPSREVAICLDPYCGLGFVLWCLCSVYSGHQSI
+LIPPSELETNPALWLLAVSQYKV
+>STRG.6.1(-)_6 [199 - 252] 
+AGNQPRLVASCRESVQSP
+>STRG.6.1(-)_7 [237 - 121] (REVERSE SENSE) 
+LTARSHKAGLVSSSEGGIRMDWCPEYTLQRHQRTNPSPQ
+>STRG.6.1(-)_8 [251 - 93] (REVERSE SENSE) 
+GLCTDSRQEATRRGWFPAQRAGSGWTGAQNTHCRGTRGQIPVHSKGPGRWPLL
+>STRG.6.1(-)_9 [117 - 85] (REVERSE SENSE) 
+GSRQMATSLEG
+>STRG.6.1(-)_10 [81 - 34] (REVERSE SENSE) 
+SSHCSLMERQKALVAA
+>STRG.6.1(-)_11 [250 - 14] (REVERSE SENSE) 
+DFVLTHGKKPQGGVGFQLRGRDQDGLVPRIHTAEAPEDKSQSTVRVQADGHFSRGVKFTL
+QLNGTAEGTGGCVRHLYAS
+>STRG.6.1(-)_12 [62 - 3] (REVERSE SENSE) 
+WNGRRHWWLRETSLRQLASQ
+>STRG.6.1(-)_13 [30 - 1] (REVERSE SENSE) 
+DIFTPASIPV
+>STRG.8.1(-)_1 [18 - 56] 
+RTSKKPNGRDPTV
+>STRG.8.1(-)_2 [60 - 95] 
+RLAKAAVVCHRV
+>STRG.8.1(-)_3 [99 - 137] 
+TSLQTAPRLVPTH
+>STRG.8.1(-)_4 [2 - 205] 
+VTPAIKDFQKAQRERSHSLKVGQSCCGLSQSLNISPNRPETGSHTLKMPITTLRILSTRR
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output.fasta	Mon Aug 07 13:52:15 2023 +0000
@@ -0,0 +1,6 @@
+>STRG.4.1(-)_12 [1 - 666]
+DPTTVYVDMRALRHDRVRLVERGSPHSLPLMESGKILPGVRIIIANPETKGPLGDSHLGEIWVHSAHNASGYFTIYGDESLQSDHFNSRLSFGDTQTIWARTGYLGFLRRTELTDANGERHDALYVVGALDEAMELRGMRYHPIDIETSVIRAHKSVTECAVFTWTNLLVVVVELDGSEQEALDLVPLVTNVVLEEHYLIVGVVVVVDIGVIPINSRGEKQR
+>STRG.6.1(-)_5 [2 - 250]
+TGMLAGVKMSHAATSAFCRSIKLQCELYPSREVAICLDPYCGLGFVLWCLCSVYSGHQSILIPPSELETNPALWLLAVSQYKV
+>STRG.8.1(-)_4 [2 - 205]
+VTPAIKDFQKAQRERSHSLKVGQSCCGLSQSLNISPNRPETGSHTLKMPITTLRILSTRR
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output.tab	Mon Aug 07 13:52:15 2023 +0000
@@ -0,0 +1,46 @@
+seqID	transcript	orf_start	orf_end	length	strand	sense	longest
+STRG.4.1(-)_1	STRG.4.1	3	77	74	-	normal	n
+STRG.4.1(-)_2	STRG.4.1	59	88	29	-	normal	n
+STRG.4.1(-)_3	STRG.4.1	92	127	35	-	normal	n
+STRG.4.1(-)_4	STRG.4.1	131	268	137	-	normal	n
+STRG.4.1(-)_5	STRG.4.1	81	332	251	-	normal	n
+STRG.4.1(-)_6	STRG.4.1	272	379	107	-	normal	n
+STRG.4.1(-)_7	STRG.4.1	366	437	71	-	normal	n
+STRG.4.1(-)_8	STRG.4.1	465	518	53	-	normal	n
+STRG.4.1(-)_9	STRG.4.1	383	565	182	-	normal	n
+STRG.4.1(-)_10	STRG.4.1	599	664	65	-	normal	n
+STRG.4.1(-)_11	STRG.4.1	522	665	143	-	normal	n
+STRG.4.1(-)_12	STRG.4.1	1	666	665	-	normal	y
+STRG.4.1(-)_13	STRG.4.1	665	594	71	-	reverse_sense	n
+STRG.4.1(-)_14	STRG.4.1	631	491	140	-	reverse_sense	n
+STRG.4.1(-)_15	STRG.4.1	590	375	215	-	reverse_sense	n
+STRG.4.1(-)_16	STRG.4.1	448	341	107	-	reverse_sense	n
+STRG.4.1(-)_17	STRG.4.1	371	312	59	-	reverse_sense	n
+STRG.4.1(-)_18	STRG.4.1	666	271	395	-	reverse_sense	n
+STRG.4.1(-)_19	STRG.4.1	337	260	77	-	reverse_sense	n
+STRG.4.1(-)_20	STRG.4.1	308	255	53	-	reverse_sense	n
+STRG.4.1(-)_21	STRG.4.1	256	224	32	-	reverse_sense	n
+STRG.4.1(-)_22	STRG.4.1	246	169	77	-	reverse_sense	n
+STRG.4.1(-)_23	STRG.4.1	217	128	89	-	reverse_sense	n
+STRG.4.1(-)_24	STRG.4.1	188	78	110	-	reverse_sense	n
+STRG.4.1(-)_25	STRG.4.1	165	58	107	-	reverse_sense	n
+STRG.4.1(-)_26	STRG.4.1	74	18	56	-	reverse_sense	n
+STRG.4.1(-)_27	STRG.4.1	124	2	122	-	reverse_sense	n
+STRG.4.1(-)_28	STRG.4.1	54	1	53	-	reverse_sense	n
+STRG.6.1(-)_1	STRG.6.1	1	63	62	-	normal	n
+STRG.6.1(-)_2	STRG.6.1	24	182	158	-	normal	n
+STRG.6.1(-)_3	STRG.6.1	94	195	101	-	normal	n
+STRG.6.1(-)_4	STRG.6.1	186	233	47	-	normal	n
+STRG.6.1(-)_5	STRG.6.1	2	250	248	-	normal	y
+STRG.6.1(-)_6	STRG.6.1	199	252	53	-	normal	n
+STRG.6.1(-)_7	STRG.6.1	237	121	116	-	reverse_sense	n
+STRG.6.1(-)_8	STRG.6.1	251	93	158	-	reverse_sense	n
+STRG.6.1(-)_9	STRG.6.1	117	85	32	-	reverse_sense	n
+STRG.6.1(-)_10	STRG.6.1	81	34	47	-	reverse_sense	n
+STRG.6.1(-)_11	STRG.6.1	250	14	236	-	reverse_sense	n
+STRG.6.1(-)_12	STRG.6.1	62	3	59	-	reverse_sense	n
+STRG.6.1(-)_13	STRG.6.1	30	1	29	-	reverse_sense	n
+STRG.8.1(-)_1	STRG.8.1	18	56	38	-	normal	n
+STRG.8.1(-)_2	STRG.8.1	60	95	35	-	normal	n
+STRG.8.1(-)_3	STRG.8.1	99	137	38	-	normal	n
+STRG.8.1(-)_4	STRG.8.1	2	205	203	-	normal	y