Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 482398) +++ head/biology/Makefile (revision 482399) @@ -1,147 +1,148 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell + SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/py-pyfaidx/Makefile =================================================================== --- head/biology/py-pyfaidx/Makefile (nonexistent) +++ head/biology/py-pyfaidx/Makefile (revision 482399) @@ -0,0 +1,21 @@ +# $FreeBSD$ + +PORTNAME= pyfaidx +DISTVERSION= 0.5.5.1 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Efficient pythonic random access to fasta subsequences + +LICENSE= BSD3CLAUSE + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} + +USES= python +USE_PYTHON= distutils concurrent autoplist + +NO_ARCH= yes + +.include Property changes on: head/biology/py-pyfaidx/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/py-pyfaidx/distinfo =================================================================== --- head/biology/py-pyfaidx/distinfo (nonexistent) +++ head/biology/py-pyfaidx/distinfo (revision 482399) @@ -0,0 +1,3 @@ +TIMESTAMP = 1539913803 +SHA256 (pyfaidx-0.5.5.1.tar.gz) = d216924c901f39d445e13e574583442cd09f67424e13c2d33a5aacdfd367d39d +SIZE (pyfaidx-0.5.5.1.tar.gz) = 30205 Property changes on: head/biology/py-pyfaidx/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/py-pyfaidx/pkg-descr =================================================================== --- head/biology/py-pyfaidx/pkg-descr (nonexistent) +++ head/biology/py-pyfaidx/pkg-descr (revision 482399) @@ -0,0 +1,13 @@ +FASTA is a format to exchange generic information, partial or of the entire +organism. + +A function "faidx" (FAsta InDeX) creates a small flat index file ".fai" allowing +for fast random access to any subsequence in the indexed FASTA file, while +loading a minimal amount of the file in to memory. This python module implements +pure Python classes for indexing, retrieval, and in-place modification of FASTA +files using a samtools compatible index. The pyfaidx module is API compatible +with the pygr seqdb module. A command-line script "faidx" is installed alongside +the pyfaidx module, and facilitates complex manipulation of FASTA files without +any programming knowledge. + +WWW: https://github.com/mdshw5/pyfaidx Property changes on: head/biology/py-pyfaidx/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property