# HG changeset patch # User peterjc # Date 1366043331 14400 # Node ID 28d52478ace9e934572f56066e95cb4caf25d487 # Parent 50a8a6917a9c4a0562670397127c6a9fc59ac620 Uploaded v0.0.4 which adds a unit test. diff -r 50a8a6917a9c -r 28d52478ace9 test-data/k12_hypothetical.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/k12_hypothetical.fasta Mon Apr 15 12:28:51 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 50a8a6917a9c -r 28d52478ace9 test-data/k12_hypothetical.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/k12_hypothetical.tabular Mon Apr 15 12:28:51 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 50a8a6917a9c -r 28d52478ace9 test-data/k12_ten_proteins.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/k12_ten_proteins.fasta Mon Apr 15 12:28:51 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 50a8a6917a9c -r 28d52478ace9 tools/filters/seq_select_by_id.py --- a/tools/filters/seq_select_by_id.py Fri May 18 12:25:12 2012 -0400 +++ b/tools/filters/seq_select_by_id.py Mon Apr 15 12:28:51 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 2011-2012 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 0.0.3 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:] diff -r 50a8a6917a9c -r 28d52478ace9 tools/filters/seq_select_by_id.txt --- a/tools/filters/seq_select_by_id.txt Fri May 18 12:25:12 2012 -0400 +++ b/tools/filters/seq_select_by_id.txt Mon Apr 15 12:28:51 2013 -0400 @@ -35,7 +35,10 @@ ======= v0.0.1 - Initial version. -v0.0.3 - Ignore blank lines in input +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 50a8a6917a9c -r 28d52478ace9 tools/filters/seq_select_by_id.xml --- a/tools/filters/seq_select_by_id.xml Fri May 18 12:25:12 2012 -0400 +++ b/tools/filters/seq_select_by_id.xml Mon Apr 15 12:28:51 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 +23,12 @@ + + + + + + Bio