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        "description": "SCRAM\n-----\n\n--------------\n\nSCRAM is lightweight Python package for aligning small RNA reads to one\nor more reference sequences and producing publication-quality images.\n\nDeveloped by Stephen Fletcher @ the laboratory of Prof. Bernie Carroll,\nUniversity of Queensland\n\n--------------\n\n*Installation:*\n\nScram is written in Python 2.7. Install scram and its dependencies with\n``pip``:\n\n``pip install scram``\n\nOr download and extract the tarball, then run:\n\n``python setup.py install``\n\n--------------\n\n*Input File Format:*\n\nReference File : DNA nucleotides only (AGCT) - FASTA format\n\nSequence File : Collapsed reads - DNA nucleotides only (AGCT) - FASTA\nformat\n\nPost-processing of FASTQ reads to collapsed FASTA format can be carried\nout using the `FASTX-Toolkit from the Hannon\nLab <http://hannonlab.cshl.edu/fastx_toolkit/>`__. Collapsed reads are\nunique, and contain the read count in the header.\n\nAn example of the required read file format:\n\n``head seq1.fa``\n\n::\n\n    >1-607041\n    TCGGACCAGGCATCATTCCCC\n    >2-202886\n    TCGGACCAGGCTTCATACCCC\n    >3-71446\n    TCCCAAATATAGACAAAGCA\n\n--------------\n\n*Usage:*\n\n``scram analysis_type reference_file [-h] [-s1 SEQ_FILE_1] [-s2 SEQ_FILE_2] [-s3 SEQ_FILE_3] [-s4 SEQ_FILE_4] [-nt SRNA_LEN] [-f FILE_NAME] [-seq_list SEQ_LIST] [-min_read MIN_READ_SIZE] [-max_read MAX_READ_SIZE] [-min_count MIN_READ_COUNT] [-win SMOOTH_WIN_SIZE] [-ylim YLIM] [-no_display] [-split] [-pub] [-V]``\n\nAnalysis types\n\n-  **den** : align reads of a single sRNA class (eg. 21 nt) from a\n   single sequence file to a single reference sequence (-s1 and -nt\n   required)\n-  **mnt3dm** : align 21, 22 and 24 nt reads from a single sequence file\n   to a single reference sequence (-s1 required)\n-  **CDP** : count aligned reads of a single sRNA class (eg. 21 nt) to\n   multiple reference sequences. Counts for two sequence files are\n   plotted as (x,y) coordinates for each reference (-s1, -s2 and -nt\n   required)\n\nFlags\n\n-  **-h** : Help message\n-  **-s1** : Sequence file 1\n-  **-s2** : Sequence file 2\n-  **-s3** : Sequence file 3\n-  **-s4** : Sequence file 4\n-  **-nt** : sRNA length to analyse\n-  **-f** : Figure output file name (if not auto-generated)\n-  **-p** : Number of cores (processors) to use (default=4)\n-  **-seq\\_list** : Text (.txt) file with full path of sequence file on\n   each line (single replicate) or two tab-delimited sequence file paths\n   per line (two replicates)\n-  **-min\\_read** : Minimum length of sRNA reads used for normalisation\n   (default=18)\n-  **-max\\_read** : Maximum length of sRNA reads used for normalisation\n   (default=32)\n-  **-min\\_count** : Minimum read count for an sRNA to be aligned and\n   used for normalisation (default=1)\n-  **-win** : Window size for smoothing of den plots (default=50)\n-  **-ylim** : +/- y-axis limit on plots\n-  **-no\\_display** : Do not display plot on screen\n-  **-no\\_csv** : Do not generate .csv alignment file\n-  **-split** : Split CDP read alignment counts based on no. of\n   alignments\n-  **-pub** : Remove all labels from density maps for publication\n-  **-V** : Show program's version number and exit\n\n--------------\n\nden example:\n\n``scram den ./ref.fa -s1 seq1.fa -nt 24 -win 30 -f fig1.pdf``\n\nmnt3dm Example:\n\n``scram mnt3dm ./ref.fa -s1 seq1.fa -win 20 -ylim 110 -f fig2.pdf``\n\nCDP Example:\n\n``scram CDP ./cDNAs.fa -s1 seq1.fa -s2 seq2.fa -nt 21 -f fig3.pdf -split``\n\n--------------\n\n(c) 2016 - Stephen Fletcher. MIT License\n                                        \n",
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