# HG changeset patch
# User peterjc
# Date 1365762024 14400
# Node ID cfae9b16ab6540855b45be0c53c061ec984d0a92
# Parent 2b27279adeff0e1657f7da7609b1c55727aecfc7
Uploaded v0.0.4
diff -r 2b27279adeff -r cfae9b16ab65 test-data/k12_hypothetical.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/k12_hypothetical.fasta Fri Apr 12 06:20:24 2013 -0400
@@ -0,0 +1,3 @@
+>gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli str. K-12 substr. MG1655]
+MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGWWKQHYEWRGNRWHL
+HGPPPPPRHHKKAPHDHHGGHGPGKHHR
diff -r 2b27279adeff -r cfae9b16ab65 test-data/k12_hypothetical.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/k12_hypothetical.tabular Fri Apr 12 06:20:24 2013 -0400
@@ -0,0 +1,2 @@
+#ID Description
+gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli str. K-12 substr. MG1655]
diff -r 2b27279adeff -r cfae9b16ab65 test-data/k12_ten_proteins.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/k12_ten_proteins.fasta Fri Apr 12 06:20:24 2013 -0400
@@ -0,0 +1,60 @@
+>gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia coli str. K-12 substr. MG1655]
+MKRISTTITTTITITTGNGAG
+>gi|16127996|ref|NP_414543.1| fused aspartokinase I and homoserine dehydrogenase I [Escherichia coli str. K-12 substr. MG1655]
+MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERI
+FAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEA
+RGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYS
+AAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPC
+LIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLIT
+QSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
+ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSW
+LKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV
+ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELM
+KFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIE
+IEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFK
+VKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
+>gi|16127997|ref|NP_414544.1| homoserine kinase [Escherichia coli str. K-12 substr. MG1655]
+MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWE
+RFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHY
+DNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGF
+IHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVA
+DWLGKNYLQNQEGFVHICRLDTAGARVLEN
+>gi|16127998|ref|NP_414545.1| threonine synthase [Escherichia coli str. K-12 substr. MG1655]
+MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQE
+ILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAA
+VAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNS
+ANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVP
+RFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTS
+EPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL
+RKLMMNHQ
+>gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli str. K-12 substr. MG1655]
+MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGWWKQHYEWRGNRWHL
+HGPPPPPRHHKKAPHDHHGGHGPGKHHR
+>gi|16128000|ref|NP_414547.1| peroxide resistance protein, lowers intracellular iron [Escherichia coli str. K-12 substr. MG1655]
+MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINAARFHDWQPD
+FTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARG
+KDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKK
+ARGLMSRFIIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR
+>gi|16128001|ref|NP_414548.1| putative transporter [Escherichia coli str. K-12 substr. MG1655]
+MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTSFQSLCTSLAA
+RVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMR
+WMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPL
+MAIIWVLTSLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPN
+AAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAE
+FVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMACMA
+ITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE
+>gi|16128002|ref|NP_414549.1| transaldolase B [Escherichia coli str. K-12 substr. MG1655]
+MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAKQQSNDRAQQI
+VDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGI
+RAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIY
+QYYKEHGYETVVMGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESE
+FLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL
+>gi|16128003|ref|NP_414550.1| molybdochelatase incorporating molybdenum into molybdopterin [Escherichia coli str. K-12 substr. MG1655]
+MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELVDEMSCHLV
+LTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIK
+ETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE
+>gi|16128004|ref|NP_414551.1| inner membrane protein, Grp1_Fun34_YaaH family [Escherichia coli str. K-12 substr. MG1655]
+MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNTFGLTAFT
+SYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGARVLQFVFFSLTVLFALLAI
+GNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLPIGESH
+
diff -r 2b27279adeff -r cfae9b16ab65 tools/filters/seq_select_by_id.py
--- a/tools/filters/seq_select_by_id.py Tue Jun 07 17:13:04 2011 -0400
+++ b/tools/filters/seq_select_by_id.py Fri Apr 12 06:20:24 2013 -0400
@@ -16,11 +16,11 @@
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-This script is copyright 2011 by Peter Cock, The James Hutton Institute UK.
+This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
All rights reserved. See accompanying text file for licence details (MIT/BSD
style).
-This is version 0.0.1 of the script.
+This is version 0.0.4 of the script.
"""
import sys
@@ -28,6 +28,10 @@
sys.stderr.write(msg.rstrip() + "\n")
sys.exit(err)
+if "-v" in sys.argv or "--version" in sys.argv:
+ print "v0.0.4"
+ sys.exit(0)
+
#Parse Command Line
try:
tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:]
@@ -39,7 +43,7 @@
else:
column = int(col_arg)-1
except ValueError:
- stop_err("Expected column number, got %s" % cols_arg)
+ stop_err("Expected column number, got %s" % col_arg)
if seq_format == "fastqcssanger":
stop_err("Colorspace FASTQ not supported.")
@@ -65,7 +69,7 @@
"""Read tabular file and record all specified identifiers."""
handle = open(tabular_file, "rU")
for line in handle:
- if not line.startswith("#"):
+ if line.strip() and not line.startswith("#"):
yield line.rstrip("\n").split("\t")[col].strip()
handle.close()
@@ -105,7 +109,7 @@
except KeyError, err:
out_handle.close()
if name not in records:
- stop_err("Identifier %s not found in sequence file" % name)
+ stop_err("Identifier %r not found in sequence file" % name)
else:
raise err
out_handle.close()
@@ -119,7 +123,7 @@
out_handle.write(records.get_raw(name))
except KeyError:
out_handle.close()
- stop_err("Identifier %s not found in sequence file" % name)
+ stop_err("Identifier %r not found in sequence file" % name)
count += 1
out_handle.close()
diff -r 2b27279adeff -r cfae9b16ab65 tools/filters/seq_select_by_id.txt
--- a/tools/filters/seq_select_by_id.txt Tue Jun 07 17:13:04 2011 -0400
+++ b/tools/filters/seq_select_by_id.txt Fri Apr 12 06:20:24 2013 -0400
@@ -1,5 +1,5 @@
-Galaxy tool to select FASTA, FASTQ or SFF sequences by ID
-=========================================================
+Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
+===============================================================
This tool is copyright 2011 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
@@ -26,7 +26,7 @@
You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
tool. One suggested location is in the filters section. Simply add the line:
-
+
You will also need to install Biopython 1.54 or later. That's it.
@@ -35,6 +35,9 @@
=======
v0.0.1 - Initial version.
+v0.0.3 - Ignore blank lines in input.
+v0.0.4 - Record script version when run from Galaxy.
+ - Basic unit test included.
Developers
@@ -43,10 +46,10 @@
This script and related tools are being developed on the following hg branch:
http://bitbucket.org/peterjc/galaxy-central/src/tools
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder:
-tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.*
+$ tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
Check this worked:
@@ -54,6 +57,9 @@
filter/seq_select_by_id.py
filter/seq_select_by_id.txt
filter/seq_select_by_id.xml
+test-data/k12_ten_proteins.fasta
+test-data/k12_hypothetical.fasta
+test-data/k12_hypothetical.tabular
Licence (MIT/BSD style)
diff -r 2b27279adeff -r cfae9b16ab65 tools/filters/seq_select_by_id.xml
--- a/tools/filters/seq_select_by_id.xml Tue Jun 07 17:13:04 2011 -0400
+++ b/tools/filters/seq_select_by_id.xml Fri Apr 12 06:20:24 2013 -0400
@@ -1,5 +1,6 @@
-
+
from a tabular file
+ seq_select_by_id.py --version
seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
@@ -22,6 +23,10 @@
+
+
+
+
Bio